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Simply, tandem repeats are shorter than SINE elements. Both are suspected of playing a role in creating the plethora of dog breeds. But changes in the timing of development are also believed to be involved. Sorting that out is where the Dog Genome Project began and where it still must go. In that sense, the genome sequence represents a beginning rather than an end.

A Genomic Look at History
It is often remarked and lamented that despite, in some cases, centuries of inbreeding and use of “favored sires” year after year, litter after litter, even the most purebred of dogs continue to show variability in terms of appearance and behavior. In other words, they don’t always breed “true” to the breeder’s desire. In behavioral terms, as John Paul Scott and John L. Fuller observed 40 years ago in their seminal book, Genetics and the Social Behavior of the Dog, through selective breeding, humans have concentrated different aspects of wolf behavior in dog breeds so that each one represents “one of many possible individual behavioral variations.” Yet Scott and Fuller also pointed out that for all the specialization, there is often greater variability in terms of temperament and talent between dogs within a breed than between breeds.

It is thus poetically fitting and perhaps scientifically significant that genetically, dogs show a similar pattern of homogeneity and variability between and within breeds, especially the modern breeds. In general, they were formed through extensive inbreeding and the use of favored sires, both of which serve to limit genetic diversity. Yet, despite that, or perhaps because the genetic isolation of breeds has not been long enough or as extensive as breeders sometimes claim, those breeds continue to possess a surprising amount of genetic diversity.

That diversity, in turn, makes it easier to find genes associated with various diseases and with physical appearance, as well as—it is thought—with specialized behavior. But to do that, a genetic sleuth, like a hurricane tracker, needs a map with proper coordinates, in this case SNPs.

It is easier to assemble the genomic sequence of highly inbreed animals because of the genetic homogeneity of the pairs of chromosomes being sequenced. Compared to other Boxers, Tasha’s genome has one SNP—one change in one letter, or nucleotide – every 1,600 base pairs. Less inbred breeds would have more SNPs. Such changes or mutations appear randomly throughout the genomes of all animals, primarily in non-coding regions outside genes, where their purpose, if any, is uncertain, and far less frequently within genes where they can cause lethal mutations.

SNPs persist for hundreds of generations and form distinctive, inheritable clusters or blocks of genetic code on chromosomes that are known as “haplotypes.” Because they are passed on through generations, haplotypes are useful for exploring the evolutionary history of individuals, groups and species, and seeking out clusters of genes involved in inherited diseases, in morphology and, it is hoped, behavior. Probing the differences between individuals with congenital heart disease, for example, and those without, researchers would use their SNP map to identify the haplotypes of sufferers against those who are disease-free in an effort to find a region or regions on a chromosome that seemed involved. There, they would focus the search for genes.

To create a densely detailed SNPs map of the dog genome, Dr. Lindblad-Toh’s team partially sequenced the genomes of nine additional dog breeds, four kinds of wolf, and a coyote: German Shepherd, Rottweiler, Bedlington Terrier, Beagle, Labrador Retriever, English Shepherd, Italian Greyhound, Alaskan Malamute, Portuguese Water Dog, Chinese gray wolf, Alaskan gray wolf, Indian gray wolf, Spanish gray wolf, and California coyote. They also had the genome sequence from the French Poodle, Shadow. The researchers found 2.5 million cases where there were differences in a single nucleotide between the various canine genomes.